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-rwxr-xr-xwqflask/wqflask/interval_mapping/interval_mapping.py97
-rwxr-xr-xwqflask/wqflask/marker_regression/marker_regression.py1
-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/lmm.py2
-rw-r--r--wqflask/wqflask/static/new/css/interval_mapping.css21
-rw-r--r--wqflask/wqflask/static/new/css/marker_regression.css4
-rw-r--r--wqflask/wqflask/static/new/javascript/bar_chart.coffee326
-rw-r--r--wqflask/wqflask/static/new/javascript/bar_chart.js196
-rw-r--r--wqflask/wqflask/static/new/javascript/dataset_select_menu.coffee2
-rw-r--r--wqflask/wqflask/static/new/javascript/dataset_select_menu.js2
-rw-r--r--wqflask/wqflask/static/new/javascript/get_traits_from_collection.coffee10
-rw-r--r--wqflask/wqflask/static/new/javascript/get_traits_from_collection.js10
-rw-r--r--wqflask/wqflask/static/new/javascript/interval_mapping.coffee70
-rw-r--r--wqflask/wqflask/static/new/javascript/interval_mapping.js31
-rw-r--r--wqflask/wqflask/static/new/javascript/marker_regression.coffee8
-rw-r--r--wqflask/wqflask/static/new/javascript/marker_regression.js7
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait.coffee9
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait.js7
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee5
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js7
-rw-r--r--wqflask/wqflask/templates/collections/list.html2
-rw-r--r--wqflask/wqflask/templates/interval_mapping.html15
-rw-r--r--wqflask/wqflask/templates/show_trait.html6
-rw-r--r--wqflask/wqflask/templates/show_trait_mapping_tools.html16
-rw-r--r--wqflask/wqflask/templates/show_trait_statistics_new.html22
-rw-r--r--wqflask/wqflask/views.py1
25 files changed, 599 insertions, 278 deletions
diff --git a/wqflask/wqflask/interval_mapping/interval_mapping.py b/wqflask/wqflask/interval_mapping/interval_mapping.py
index de7a2704..f0985cc2 100755
--- a/wqflask/wqflask/interval_mapping/interval_mapping.py
+++ b/wqflask/wqflask/interval_mapping/interval_mapping.py
@@ -37,8 +37,6 @@ class IntervalMapping(object):
def __init__(self, start_vars, temp_uuid):
- print("TESTING!!!")
-
#Currently only getting trait data for one trait, but will need
#to change this to accept multiple traits once the collection page is implemented
helper_functions.get_species_dataset_trait(self, start_vars)
@@ -57,7 +55,11 @@ class IntervalMapping(object):
self.set_options(start_vars)
- self.gen_qtl_results(tempdata)
+ if self.method == "qtl_reaper":
+ self.gen_reaper_results(tempdata)
+ else:
+ self.gen_pylmm_results(tempdata)
+ #self.gen_qtl_results(tempdata)
#Get chromosome lengths for drawing the interval map plot
chromosome_mb_lengths = {}
@@ -78,6 +80,7 @@ class IntervalMapping(object):
#self.plot_scale = start_vars['scale']
#if self.plotScale == 'physic' and not fd.genotype.Mbmap:
# self.plotScale = 'morgan'
+ self.method = start_vars['mapping_method']
self.num_permutations = int(start_vars['num_permutations'])
#self.do_bootstrap = start_vars['do_bootstrap']
self.selected_chr = start_vars['chromosome']
@@ -125,9 +128,6 @@ class IntervalMapping(object):
# variance = variances,
# control = self.control_locus)
#else:
- #reaper_results = self.dataset.group.genotype.regression(strains = trimmed_samples,
- # trait = trimmed_values,
- # control = self.control_locus)
reaper_results = genotype.regression(strains = trimmed_samples,
trait = trimmed_values,
control = self.control_locus)
@@ -139,8 +139,6 @@ class IntervalMapping(object):
#else:
print("strains:", trimmed_samples)
print("trait:", trimmed_values)
- #reaper_results = self.dataset.group.genotype.regression(strains = trimmed_samples,
- # trait = trimmed_values)
reaper_results = genotype.regression(strains = trimmed_samples,
trait = trimmed_values)
@@ -152,29 +150,70 @@ class IntervalMapping(object):
qtl = {"lrs": qtl.lrs, "locus": locus, "additive": qtl.additive}
self.qtl_results.append(qtl)
- #pheno_vector = np.array([val == "x" and np.nan or float(val) for val in self.vals])
- #if self.dataset.group.species == "human":
- # p_values, t_stats = self.gen_human_results(pheno_vector, tempdata)
- #else:
- #genotype_data = [marker['genotypes'] for marker in self.dataset.group.markers.markers]
- #
- #no_val_samples = self.identify_empty_samples()
- #trimmed_genotype_data = self.trim_genotypes(genotype_data, no_val_samples)
- #
- #genotype_matrix = np.array(trimmed_genotype_data).T
-
- #t_stats, p_values = lmm.run(
- # pheno_vector,
- # genotype_matrix,
- # restricted_max_likelihood=True,
- # refit=False,
- # temp_data=tempdata
- #)
-
- #self.dataset.group.markers.add_pvalues(p_values)
+ def gen_reaper_results(self, tempdata):
+ genotype = self.dataset.group.read_genotype_file()
+
+ samples, values, variances = self.this_trait.export_informative()
+
+ trimmed_samples = []
+ trimmed_values = []
+ for i in range(0, len(samples)):
+ if samples[i] in self.dataset.group.samplelist:
+ trimmed_samples.append(samples[i])
+ trimmed_values.append(values[i])
+
+ self.lrs_array = genotype.permutation(strains = trimmed_samples,
+ trait = trimmed_values,
+ nperm= self.num_permutations)
+ self.suggestive = self.lrs_array[int(self.num_permutations*0.37-1)]
+ self.significant = self.lrs_array[int(self.num_permutations*0.95-1)]
+
+ print("samples:", trimmed_samples)
+
+ if self.control_locus:
+ reaper_results = genotype.regression(strains = trimmed_samples,
+ trait = trimmed_values,
+ control = self.control_locus)
+ else:
+ reaper_results = genotype.regression(strains = trimmed_samples,
+ trait = trimmed_values)
+
+ #Need to convert the QTL objects that qtl reaper returns into a json serializable dictionary
+ self.qtl_results = []
+ for qtl in reaper_results:
+ reaper_locus = qtl.locus
+ locus = {"name":reaper_locus.name, "chr":reaper_locus.chr, "cM":reaper_locus.cM, "Mb":reaper_locus.Mb}
+ qtl = {"lrs_value": qtl.lrs, "chr":reaper_locus.chr, "Mb":reaper_locus.Mb,
+ "cM":reaper_locus.cM, "name":reaper_locus.name, "additive":qtl.additive}
+ self.qtl_results.append(qtl)
+
+ def gen_pylmm_results(self, tempdata):
+ print("USING PYLMM")
+ self.dataset.group.get_markers()
- #self.qtl_results = self.dataset.group.markers.markers
+ pheno_vector = np.array([val == "x" and np.nan or float(val) for val in self.vals])
+ if self.dataset.group.species == "human":
+ p_values, t_stats = self.gen_human_results(pheno_vector, tempdata)
+ else:
+ genotype_data = [marker['genotypes'] for marker in self.dataset.group.markers.markers]
+
+ no_val_samples = self.identify_empty_samples()
+ trimmed_genotype_data = self.trim_genotypes(genotype_data, no_val_samples)
+
+ genotype_matrix = np.array(trimmed_genotype_data).T
+
+ t_stats, p_values = lmm.run(
+ pheno_vector,
+ genotype_matrix,
+ restricted_max_likelihood=True,
+ refit=False,
+ temp_data=tempdata
+ )
+
+ print("p_values:", p_values)
+ self.dataset.group.markers.add_pvalues(p_values)
+ self.qtl_results = self.dataset.group.markers.markers
def gen_qtl_results_2(self, tempdata):
"""Generates qtl results for plotting interval map"""
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 334ce631..006c586b 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -91,7 +91,6 @@ class MarkerRegression(object):
)
self.dataset.group.markers.add_pvalues(p_values)
-
self.qtl_results = self.dataset.group.markers.markers
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
index 6ef1669b..60d36b8d 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
@@ -107,8 +107,6 @@ def run_human(pheno_vector,
with Bench("Create list of inputs"):
inputs = list(plink_input)
-
- print("len(genotypes): ", len(inputs))
with Bench("Divide into chunks"):
results = chunks.divide_into_chunks(inputs, 64)
diff --git a/wqflask/wqflask/static/new/css/interval_mapping.css b/wqflask/wqflask/static/new/css/interval_mapping.css
index 9d23ba25..5ebf7742 100644
--- a/wqflask/wqflask/static/new/css/interval_mapping.css
+++ b/wqflask/wqflask/static/new/css/interval_mapping.css
@@ -1,27 +1,32 @@
-.manhattan_plot .y_axis path,
-.manhattan_plot .y_axis line {
+.interval_map .y_axis path,
+.interval_map .y_axis line {
fill: none;
stroke: black;
shape-rendering: crispEdges;
}
-.manhattan_plot .y_axis text {
+.interval_map .y_axis text {
font-family: sans-serif;
font-size: 14px;
}
-.manhattan_plot .x_axis path,
-.manhattan_plot .x_axis line {
+.interval_map .x_axis path,
+.interval_map .x_axis line {
fill: none;
stroke: black;
shape-rendering: crispEdges;
}
-.manhattan_plot .x_axis text {
+.interval_map .x_axis text {
text-anchor: end;
font-family: sans-serif;
font-size: 8px;
}
-rect {
+interval_map rect {
stroke: WhiteSmoke;
- fill: lightgrey;
+ fill: white;
+}
+
+interval_map path {
+ stroke: steelblue;
+ stroke-width: 1;
} \ No newline at end of file
diff --git a/wqflask/wqflask/static/new/css/marker_regression.css b/wqflask/wqflask/static/new/css/marker_regression.css
index 054ef93e..a737c97e 100644
--- a/wqflask/wqflask/static/new/css/marker_regression.css
+++ b/wqflask/wqflask/static/new/css/marker_regression.css
@@ -21,10 +21,10 @@
font-size: 8px;
}
-rect {
+/*rect {
stroke: WhiteSmoke;
fill: lightgrey;
-}
+}*/
/*rect {
stroke: WhiteSmoke;
fill: Azure;
diff --git a/wqflask/wqflask/static/new/javascript/bar_chart.coffee b/wqflask/wqflask/static/new/javascript/bar_chart.coffee
index 412185d8..e1bb36e1 100644
--- a/wqflask/wqflask/static/new/javascript/bar_chart.coffee
+++ b/wqflask/wqflask/static/new/javascript/bar_chart.coffee
@@ -2,11 +2,12 @@ root = exports ? this
class Bar_Chart
constructor: (@sample_list, @sample_group) ->
+ @sort_by = "name"
@get_samples()
console.log("sample names:", @sample_names)
if @sample_attr_vals.length > 0
@get_distinct_attr_vals()
- @get_attr_color_dict()
+ @get_attr_color_dict(@distinct_attr_vals)
#Used to calculate the bottom margin so sample names aren't cut off
longest_sample_name = d3.max(sample.length for sample in @sample_names)
@@ -28,17 +29,19 @@ class Bar_Chart
@create_graph()
d3.select("#color_attribute").on("change", =>
- attribute = $("#color_attribute").val()
- if $("#update_bar_chart").html() == 'Sort By Name'
+ @attribute = $("#color_attribute").val()
+ console.log("attr_color_dict:", @attr_color_dict)
+ #if $("#update_bar_chart").html() == 'Sort By Name'
+ if @sort_by = "name"
@svg.selectAll(".bar")
.data(@sorted_samples())
.transition()
.duration(1000)
.style("fill", (d) =>
- if attribute == "None"
+ if @attribute == "None"
return "steelblue"
else
- return @attr_color_dict[attribute][d[2][attribute]]
+ return @attr_color_dict[@attribute][d[2][@attribute]]
)
.select("title")
.text((d) =>
@@ -50,86 +53,196 @@ class Bar_Chart
.transition()
.duration(1000)
.style("fill", (d) =>
- if attribute == "None"
+ if @attribute == "None"
return "steelblue"
else
- return @attr_color_dict[attribute][d[2][attribute]]
+ return @attr_color_dict[@attribute][d[2][@attribute]]
)
- @add_legend(attribute, @distinct_attr_vals[attribute])
+ @add_legend(@attribute, @distinct_attr_vals[@attribute])
)
-
-
- d3.select("#update_bar_chart").on("click", =>
- if @attributes.length > 0
- attribute = $("#color_attribute").val()
- if $("#update_bar_chart").html() == 'Sort By Value'
- $("#update_bar_chart").html('Sort By Name')
- sortItems = (a, b) ->
- return a[1] - b[1]
- @svg.selectAll(".bar")
- .data(@sorted_samples())
- .transition()
- .duration(1000)
- .attr("y", (d) =>
- return @y_scale(d[1])
- )
- .attr("height", (d) =>
- return @plot_height - @y_scale(d[1])
- )
- .style("fill", (d) =>
- if @attributes.length > 0
- return @attr_color_dict[attribute][d[2][attribute]]
- else
- return "steelblue"
- )
- .select("title")
- .text((d) =>
- return d[1]
- )
- sorted_sample_names = (sample[0] for sample in @sorted_samples())
- x_scale = d3.scale.ordinal()
- .domain(sorted_sample_names)
- .rangeBands([0, @plot_width], .1)
- $('.x.axis').remove()
- @add_x_axis(x_scale)
- else
- $("#update_bar_chart").html('Sort By Value')
- @svg.selectAll(".bar")
- .data(@samples)
- .transition()
- .duration(1000)
- .attr("y", (d) =>
- return @y_scale(d[1])
- )
- .attr("height", (d) =>
- return @plot_height - @y_scale(d[1])
- )
- .style("fill", (d) =>
- if @attributes.length > 0
- return @attr_color_dict[attribute][d[2][attribute]]
- else
- return "steelblue"
- )
- .select("title")
- .text((d) =>
- return d[1]
- )
- x_scale = d3.scale.ordinal()
- .domain(@sample_names)
- .rangeBands([0, @plot_width], .1)
- $('.x.axis').remove()
- @add_x_axis(x_scale)
+ $(".sort_by_value").on("click", =>
+ console.log("sorting by value")
+ @sort_by = "value"
+ if @attributes.length > 0
+ @attribute = $("#color_attribute").val()
+ #sortItems = (a, b) ->
+ # return a[1] - b[1]
+ @rebuild_bar_graph(@sorted_samples())
+ #@svg.selectAll(".bar")
+ # .data(@sorted_samples())
+ # .transition()
+ # .duration(1000)
+ # .attr("y", (d) =>
+ # return @y_scale(d[1])
+ # )
+ # .attr("height", (d) =>
+ # return @plot_height - @y_scale(d[1])
+ # )
+ # .select("title")
+ # .text((d) =>
+ # return d[1]
+ # )
+ # #.style("fill", (d) =>
+ # # if @attributes.length > 0
+ # # return @attr_color_dict[attribute][d[2][attribute]]
+ # # else
+ # # return "steelblue"
+ # #)
+ #sorted_sample_names = (sample[0] for sample in @sorted_samples())
+ #x_scale = d3.scale.ordinal()
+ # .domain(sorted_sample_names)
+ # .rangeBands([0, @plot_width], .1)
+ #$('.x.axis').remove()
+ #@add_x_axis(x_scale)
+ )
+
+ $(".sort_by_name").on("click", =>
+ console.log("sorting by name")
+ @sort_by = "name"
+ if @attributes.length > 0
+ @attribute = $("#color_attribute").val()
+ @rebuild_bar_graph(@samples)
+ #@svg.selectAll(".bar")
+ # .data(@samples)
+ # .transition()
+ # .duration(1000)
+ # .attr("y", (d) =>
+ # return @y_scale(d[1])
+ # )
+ # .attr("height", (d) =>
+ # return @plot_height - @y_scale(d[1])
+ # )
+ # .select("title")
+ # .text((d) =>
+ # return d[1]
+ # )
+ # .style("fill", (d) =>
+ # if @attributes.length > 0
+ # return @attr_color_dict[attribute][d[2][attribute]]
+ # else
+ # return "steelblue"
+ # )
+ #x_scale = d3.scale.ordinal()
+ # .domain(@sample_names)
+ # .rangeBands([0, @plot_width], .1)
+ #$('.x.axis').remove()
+ #@add_x_axis(x_scale)
)
+
+
+ #d3.select(".update_bar_chart").on("click", =>
+ # console.log("THIS IS:", $(this))
+ # sort_by = $(this).val()
+ # console.log("sort_by: ", sort_by)
+ # if @attributes.length > 0
+ # attribute = $("#color_attribute").val()
+ # if sort_by = "value"
+ # console.log("sorting by value")
+ # sortItems = (a, b) ->
+ # return a[1] - b[1]
+ #
+ # @svg.selectAll(".bar")
+ # .data(@sorted_samples())
+ # .transition()
+ # .duration(1000)
+ # .attr("y", (d) =>
+ #
+ # return @y_scale(d[1])
+ # )
+ # .attr("height", (d) =>
+ # return @plot_height - @y_scale(d[1])
+ # )
+ # .style("fill", (d) =>
+ # if @attributes.length > 0
+ # return @attr_color_dict[attribute][d[2][attribute]]
+ # else
+ # return "steelblue"
+ # )
+ # .select("title")
+ # .text((d) =>
+ # return d[1]
+ # )
+ # sorted_sample_names = (sample[0] for sample in @sorted_samples())
+ # x_scale = d3.scale.ordinal()
+ # .domain(sorted_sample_names)
+ # .rangeBands([0, @plot_width], .1)
+ # $('.x.axis').remove()
+ # @add_x_axis(x_scale)
+ # else
+ # console.log("sorting by name")
+ # #$("#update_bar_chart").html('Sort By Value')
+ # @svg.selectAll(".bar")
+ # .data(@samples)
+ # .transition()
+ # .duration(1000)
+ # .attr("y", (d) =>
+ # return @y_scale(d[1])
+ # )
+ # .attr("height", (d) =>
+ # return @plot_height - @y_scale(d[1])
+ # )
+ # .style("fill", (d) =>
+ # if @attributes.length > 0
+ # return @attr_color_dict[attribute][d[2][attribute]]
+ # else
+ # return "steelblue"
+ # )
+ # .select("title")
+ # .text((d) =>
+ # return d[1]
+ # )
+ # x_scale = d3.scale.ordinal()
+ # .domain(@sample_names)
+ # .rangeBands([0, @plot_width], .1)
+ # $('.x.axis').remove()
+ # @add_x_axis(x_scale)
+ #)
+
d3.select("#color_by_trait").on("click", =>
- @color_by_trait()
+ @open_trait_selection()
+
)
- get_attr_color_dict: () ->
+
+ rebuild_bar_graph: (samples) ->
+ console.log("samples:", samples)
+ @svg.selectAll(".bar")
+ .data(samples)
+ .transition()
+ .duration(1000)
+ .attr("y", (d) =>
+ return @y_scale(d[1])
+ )
+ .attr("height", (d) =>
+ return @plot_height - @y_scale(d[1])
+ )
+ .select("title")
+ .text((d) =>
+ return d[1]
+ )
+ .style("fill", (d) =>
+ if @attributes.length > 0 and @attribute != "None"
+ console.log("@attribute:", @attribute)
+ console.log("d[2]", d[2])
+ console.log("the_color:", @attr_color_dict[@attribute][d[2][@attribute]])
+ return @attr_color_dict[@attribute][d[2][@attribute]]
+ else
+ return "steelblue"
+ )
+ sample_names = (sample[0] for sample in samples)
+ console.log("sample_names2:", sample_names)
+ x_scale = d3.scale.ordinal()
+ .domain(sample_names)
+ .rangeBands([0, @plot_width], .1)
+ $('.x.axis').remove()
+ @add_x_axis(x_scale)
+
+ get_attr_color_dict: (vals) ->
@attr_color_dict = {}
- console.log("distinct_attr_vals:", @distinct_attr_vals)
- for own key, distinct_vals of @distinct_attr_vals
+ console.log("vals:", vals)
+ for own key, distinct_vals of vals
this_color_dict = {}
if distinct_vals.length < 10
color = d3.scale.category10()
@@ -137,6 +250,8 @@ class Bar_Chart
this_color_dict[value] = color(i)
else
console.log("distinct_values:", distinct_vals)
+ #Check whether all values are numbers, and if they are get a corresponding
+ #color gradient
if _.every(distinct_vals, (d) =>
if isNaN(d)
return false
@@ -146,13 +261,24 @@ class Bar_Chart
color_range = d3.scale.linear()
.domain([d3.min(distinct_vals),
d3.max(distinct_vals)])
- .range([0,4])
+ .range([0,255])
for value, i in distinct_vals
- console.log("color_range(value):", color_range(parseInt(value)))
- this_color_dict[value] = d3.rgb("lightblue").darker(color_range(parseInt(value)))
+ console.log("color_range(value):", parseInt(color_range(value)))
+ this_color_dict[value] = d3.rgb(parseInt(color_range(value)),0, 0)
+ #this_color_dict[value] = d3.rgb("lightblue").darker(color_range(parseInt(value)))
#this_color_dict[value] = "rgb(0, 0, " + color_range(parseInt(value)) + ")"
@attr_color_dict[key] = this_color_dict
+ convert_into_colors: (values) ->
+ color_range = d3.scale.linear()
+ .domain([d3.min(values),
+ d3.max(values)])
+ .range([0,255])
+ for value, i in values
+ console.log("color_range(value):", color_range(parseInt(value)))
+ this_color_dict[value] = d3.rgb(color_range(parseInt(value)),0, 0)
+ #this_color_dict[value] = d3.rgb("lightblue").darker(color_range(parseInt(value)))
+
get_samples: () ->
@sample_names = (sample.name for sample in @sample_list when sample.value != null)
@sample_vals = (sample.value for sample in @sample_list when sample.value != null)
@@ -304,7 +430,7 @@ class Bar_Chart
return d
)
- color_by_trait: () ->
+ open_trait_selection: () ->
$('#collections_holder').load('/collections/list?color_by_trait #collections_list', =>
$.colorbox(
inline: true
@@ -317,6 +443,50 @@ class Bar_Chart
# console.log("contents:", $(element).contents())
# $(element).contents().unwrap()
)
+
+ color_by_trait: (trait_sample_data) ->
+ console.log("BXD1:", trait_sample_data["BXD1"])
+ console.log("trait_sample_data:", trait_sample_data)
+ trimmed_samples = @trim_values(trait_sample_data)
+ distinct_values = {}
+ distinct_values["collection_trait"] = @get_distinct_values(trimmed_samples)
+ @get_attr_color_dict(distinct_values)
+ if $("#update_bar_chart").html() == 'Sort By Name'
+ @svg.selectAll(".bar")
+ .data(@sorted_samples())
+ .transition()
+ .duration(1000)
+ .style("fill", (d) =>
+ return @attr_color_dict["collection_trait"][trimmed_samples[d[0]]]
+ )
+ .select("title")
+ .text((d) =>
+ return d[1]
+ )
+ else
+ @svg.selectAll(".bar")
+ .data(@samples)
+ .transition()
+ .duration(1000)
+ .style("fill", (d) =>
+ return @attr_color_dict["collection_trait"][trimmed_samples[d[0]]]
+ )
+
+
+ trim_values: (trait_sample_data) ->
+ trimmed_samples = {}
+ for sample in @sample_names
+ if sample of trait_sample_data
+ trimmed_samples[sample] = trait_sample_data[sample]
+ console.log("trimmed_samples:", trimmed_samples)
+ return trimmed_samples
+ get_distinct_values: (samples) ->
+ distinct_values = _.uniq(_.values(samples))
+ console.log("distinct_values:", distinct_values)
+ return distinct_values
+ #distinct_values = []
+ #for sample in samples
+ # if samples[sample] in distinct_values
root.Bar_Chart = Bar_Chart \ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/bar_chart.js b/wqflask/wqflask/static/new/javascript/bar_chart.js
index e4279d41..b02ee1da 100644
--- a/wqflask/wqflask/static/new/javascript/bar_chart.js
+++ b/wqflask/wqflask/static/new/javascript/bar_chart.js
@@ -13,11 +13,12 @@
_this = this;
this.sample_list = sample_list;
this.sample_group = sample_group;
+ this.sort_by = "name";
this.get_samples();
console.log("sample names:", this.sample_names);
if (this.sample_attr_vals.length > 0) {
this.get_distinct_attr_vals();
- this.get_attr_color_dict();
+ this.get_attr_color_dict(this.distinct_attr_vals);
}
longest_sample_name = d3.max((function() {
var _i, _len, _ref, _results;
@@ -46,100 +47,94 @@
this.create_scales();
this.create_graph();
d3.select("#color_attribute").on("change", function() {
- var attribute;
- attribute = $("#color_attribute").val();
- if ($("#update_bar_chart").html() === 'Sort By Name') {
+ _this.attribute = $("#color_attribute").val();
+ console.log("attr_color_dict:", _this.attr_color_dict);
+ if (_this.sort_by = "name") {
_this.svg.selectAll(".bar").data(_this.sorted_samples()).transition().duration(1000).style("fill", function(d) {
- if (attribute === "None") {
+ if (_this.attribute === "None") {
return "steelblue";
} else {
- return _this.attr_color_dict[attribute][d[2][attribute]];
+ return _this.attr_color_dict[_this.attribute][d[2][_this.attribute]];
}
}).select("title").text(function(d) {
return d[1];
});
} else {
_this.svg.selectAll(".bar").data(_this.samples).transition().duration(1000).style("fill", function(d) {
- if (attribute === "None") {
+ if (_this.attribute === "None") {
return "steelblue";
} else {
- return _this.attr_color_dict[attribute][d[2][attribute]];
+ return _this.attr_color_dict[_this.attribute][d[2][_this.attribute]];
}
});
}
- return _this.add_legend(attribute, _this.distinct_attr_vals[attribute]);
+ return _this.add_legend(_this.attribute, _this.distinct_attr_vals[_this.attribute]);
});
- d3.select("#update_bar_chart").on("click", function() {
- var attribute, sortItems, sorted_sample_names, x_scale;
+ $(".sort_by_value").on("click", function() {
+ console.log("sorting by value");
+ _this.sort_by = "value";
if (_this.attributes.length > 0) {
- attribute = $("#color_attribute").val();
+ _this.attribute = $("#color_attribute").val();
}
- if ($("#update_bar_chart").html() === 'Sort By Value') {
- $("#update_bar_chart").html('Sort By Name');
- sortItems = function(a, b) {
- return a[1] - b[1];
- };
- _this.svg.selectAll(".bar").data(_this.sorted_samples()).transition().duration(1000).attr("y", function(d) {
- return _this.y_scale(d[1]);
- }).attr("height", function(d) {
- return _this.plot_height - _this.y_scale(d[1]);
- }).style("fill", function(d) {
- if (_this.attributes.length > 0) {
- return _this.attr_color_dict[attribute][d[2][attribute]];
- } else {
- return "steelblue";
- }
- }).select("title").text(function(d) {
- return d[1];
- });
- sorted_sample_names = (function() {
- var _i, _len, _ref, _results;
- _ref = this.sorted_samples();
- _results = [];
- for (_i = 0, _len = _ref.length; _i < _len; _i++) {
- sample = _ref[_i];
- _results.push(sample[0]);
- }
- return _results;
- }).call(_this);
- x_scale = d3.scale.ordinal().domain(sorted_sample_names).rangeBands([0, _this.plot_width], .1);
- $('.x.axis').remove();
- return _this.add_x_axis(x_scale);
- } else {
- $("#update_bar_chart").html('Sort By Value');
- _this.svg.selectAll(".bar").data(_this.samples).transition().duration(1000).attr("y", function(d) {
- return _this.y_scale(d[1]);
- }).attr("height", function(d) {
- return _this.plot_height - _this.y_scale(d[1]);
- }).style("fill", function(d) {
- if (_this.attributes.length > 0) {
- return _this.attr_color_dict[attribute][d[2][attribute]];
- } else {
- return "steelblue";
- }
- }).select("title").text(function(d) {
- return d[1];
- });
- x_scale = d3.scale.ordinal().domain(_this.sample_names).rangeBands([0, _this.plot_width], .1);
- $('.x.axis').remove();
- return _this.add_x_axis(x_scale);
+ return _this.rebuild_bar_graph(_this.sorted_samples());
+ });
+ $(".sort_by_name").on("click", function() {
+ console.log("sorting by name");
+ _this.sort_by = "name";
+ if (_this.attributes.length > 0) {
+ _this.attribute = $("#color_attribute").val();
}
+ return _this.rebuild_bar_graph(_this.samples);
});
d3.select("#color_by_trait").on("click", function() {
- return _this.color_by_trait();
+ return _this.open_trait_selection();
});
}
- Bar_Chart.prototype.get_attr_color_dict = function() {
- var color, color_range, distinct_vals, i, key, this_color_dict, value, _i, _j, _len, _len1, _ref, _results,
+ Bar_Chart.prototype.rebuild_bar_graph = function(samples) {
+ var sample, sample_names, x_scale,
+ _this = this;
+ console.log("samples:", samples);
+ this.svg.selectAll(".bar").data(samples).transition().duration(1000).attr("y", function(d) {
+ return _this.y_scale(d[1]);
+ }).attr("height", function(d) {
+ return _this.plot_height - _this.y_scale(d[1]);
+ }).select("title").text(function(d) {
+ return d[1];
+ }).style("fill", function(d) {
+ if (_this.attributes.length > 0 && _this.attribute !== "None") {
+ console.log("@attribute:", _this.attribute);
+ console.log("d[2]", d[2]);
+ console.log("the_color:", _this.attr_color_dict[_this.attribute][d[2][_this.attribute]]);
+ return _this.attr_color_dict[_this.attribute][d[2][_this.attribute]];
+ } else {
+ return "steelblue";
+ }
+ });
+ sample_names = (function() {
+ var _i, _len, _results;
+ _results = [];
+ for (_i = 0, _len = samples.length; _i < _len; _i++) {
+ sample = samples[_i];
+ _results.push(sample[0]);
+ }
+ return _results;
+ })();
+ console.log("sample_names2:", sample_names);
+ x_scale = d3.scale.ordinal().domain(sample_names).rangeBands([0, this.plot_width], .1);
+ $('.x.axis').remove();
+ return this.add_x_axis(x_scale);
+ };
+
+ Bar_Chart.prototype.get_attr_color_dict = function(vals) {
+ var color, color_range, distinct_vals, i, key, this_color_dict, value, _i, _j, _len, _len1, _results,
_this = this;
this.attr_color_dict = {};
- console.log("distinct_attr_vals:", this.distinct_attr_vals);
- _ref = this.distinct_attr_vals;
+ console.log("vals:", vals);
_results = [];
- for (key in _ref) {
- if (!__hasProp.call(_ref, key)) continue;
- distinct_vals = _ref[key];
+ for (key in vals) {
+ if (!__hasProp.call(vals, key)) continue;
+ distinct_vals = vals[key];
this_color_dict = {};
if (distinct_vals.length < 10) {
color = d3.scale.category10();
@@ -156,11 +151,11 @@
return true;
}
})) {
- color_range = d3.scale.linear().domain([d3.min(distinct_vals), d3.max(distinct_vals)]).range([0, 4]);
+ color_range = d3.scale.linear().domain([d3.min(distinct_vals), d3.max(distinct_vals)]).range([0, 255]);
for (i = _j = 0, _len1 = distinct_vals.length; _j < _len1; i = ++_j) {
value = distinct_vals[i];
- console.log("color_range(value):", color_range(parseInt(value)));
- this_color_dict[value] = d3.rgb("lightblue").darker(color_range(parseInt(value)));
+ console.log("color_range(value):", parseInt(color_range(value)));
+ this_color_dict[value] = d3.rgb(parseInt(color_range(value)), 0, 0);
}
}
}
@@ -169,6 +164,18 @@
return _results;
};
+ Bar_Chart.prototype.convert_into_colors = function(values) {
+ var color_range, i, value, _i, _len, _results;
+ color_range = d3.scale.linear().domain([d3.min(values), d3.max(values)]).range([0, 255]);
+ _results = [];
+ for (i = _i = 0, _len = values.length; _i < _len; i = ++_i) {
+ value = values[i];
+ console.log("color_range(value):", color_range(parseInt(value)));
+ _results.push(this_color_dict[value] = d3.rgb(color_range(parseInt(value)), 0, 0));
+ }
+ return _results;
+ };
+
Bar_Chart.prototype.get_samples = function() {
var attr_vals, attribute, key, sample, _i, _j, _len, _len1, _ref, _ref1;
this.sample_names = (function() {
@@ -320,7 +327,7 @@
});
};
- Bar_Chart.prototype.color_by_trait = function() {
+ Bar_Chart.prototype.open_trait_selection = function() {
var _this = this;
return $('#collections_holder').load('/collections/list?color_by_trait #collections_list', function() {
$.colorbox({
@@ -331,6 +338,49 @@
});
};
+ Bar_Chart.prototype.color_by_trait = function(trait_sample_data) {
+ var distinct_values, trimmed_samples,
+ _this = this;
+ console.log("BXD1:", trait_sample_data["BXD1"]);
+ console.log("trait_sample_data:", trait_sample_data);
+ trimmed_samples = this.trim_values(trait_sample_data);
+ distinct_values = {};
+ distinct_values["collection_trait"] = this.get_distinct_values(trimmed_samples);
+ this.get_attr_color_dict(distinct_values);
+ if ($("#update_bar_chart").html() === 'Sort By Name') {
+ return this.svg.selectAll(".bar").data(this.sorted_samples()).transition().duration(1000).style("fill", function(d) {
+ return _this.attr_color_dict["collection_trait"][trimmed_samples[d[0]]];
+ }).select("title").text(function(d) {
+ return d[1];
+ });
+ } else {
+ return this.svg.selectAll(".bar").data(this.samples).transition().duration(1000).style("fill", function(d) {
+ return _this.attr_color_dict["collection_trait"][trimmed_samples[d[0]]];
+ });
+ }
+ };
+
+ Bar_Chart.prototype.trim_values = function(trait_sample_data) {
+ var sample, trimmed_samples, _i, _len, _ref;
+ trimmed_samples = {};
+ _ref = this.sample_names;
+ for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+ sample = _ref[_i];
+ if (sample in trait_sample_data) {
+ trimmed_samples[sample] = trait_sample_data[sample];
+ }
+ }
+ console.log("trimmed_samples:", trimmed_samples);
+ return trimmed_samples;
+ };
+
+ Bar_Chart.prototype.get_distinct_values = function(samples) {
+ var distinct_values;
+ distinct_values = _.uniq(_.values(samples));
+ console.log("distinct_values:", distinct_values);
+ return distinct_values;
+ };
+
return Bar_Chart;
})();
diff --git a/wqflask/wqflask/static/new/javascript/dataset_select_menu.coffee b/wqflask/wqflask/static/new/javascript/dataset_select_menu.coffee
index 16590e26..af53bd09 100644
--- a/wqflask/wqflask/static/new/javascript/dataset_select_menu.coffee
+++ b/wqflask/wqflask/static/new/javascript/dataset_select_menu.coffee
@@ -104,7 +104,7 @@ $ ->
defaults =
species: "mouse"
group: "BXD"
- type: "Hippocampus"
+ type: "Hippocampus mRNA"
dataset: "HC_M2_0606_P"
for item in [['species', 'group']
diff --git a/wqflask/wqflask/static/new/javascript/dataset_select_menu.js b/wqflask/wqflask/static/new/javascript/dataset_select_menu.js
index 5c5b433a..3a2f044f 100644
--- a/wqflask/wqflask/static/new/javascript/dataset_select_menu.js
+++ b/wqflask/wqflask/static/new/javascript/dataset_select_menu.js
@@ -111,7 +111,7 @@
defaults = {
species: "mouse",
group: "BXD",
- type: "Hippocampus",
+ type: "Hippocampus mRNA",
dataset: "HC_M2_0606_P"
};
}
diff --git a/wqflask/wqflask/static/new/javascript/get_traits_from_collection.coffee b/wqflask/wqflask/static/new/javascript/get_traits_from_collection.coffee
index f1d41cbe..db398809 100644
--- a/wqflask/wqflask/static/new/javascript/get_traits_from_collection.coffee
+++ b/wqflask/wqflask/static/new/javascript/get_traits_from_collection.coffee
@@ -1,9 +1,11 @@
+root = exports ? this
console.log("before get_traits_from_collection")
# Going to be used to hold collection list
# So we can repopulate it when the back button is clicked
collection_list = null
+this_trait_data = null
collection_click = () ->
console.log("Clicking on:", $(this))
@@ -16,7 +18,7 @@ collection_click = () ->
url: this_collection_url,
success: process_traits
)
-
+
trait_click = () ->
console.log("Clicking on:", $(this))
trait = $(this).find('.trait').text()
@@ -28,9 +30,12 @@ trait_click = () ->
url: this_trait_url,
success: color_by_trait
)
+ $.colorbox.close()
color_by_trait = (trait_sample_data, textStatus, jqXHR) ->
- console.log('in color_by_trait:', trait_sample_data)
+ #trait_sample_data = trait_sample_data
+ #console.log('in color_by_trait:', trait_sample_data)
+ root.bar_chart.color_by_trait(trait_sample_data)
process_traits = (trait_data, textStatus, jqXHR) ->
console.log('in process_traits with trait_data:', trait_data)
@@ -65,3 +70,4 @@ $ ->
$(document).on("click", ".collection_line", collection_click)
$(document).on("click", ".trait_line", trait_click)
$(document).on("click", "#back_to_collections", back_to_collections)
+
diff --git a/wqflask/wqflask/static/new/javascript/get_traits_from_collection.js b/wqflask/wqflask/static/new/javascript/get_traits_from_collection.js
index 104c411d..fac543f8 100644
--- a/wqflask/wqflask/static/new/javascript/get_traits_from_collection.js
+++ b/wqflask/wqflask/static/new/javascript/get_traits_from_collection.js
@@ -1,11 +1,15 @@
// Generated by CoffeeScript 1.6.1
(function() {
- var back_to_collections, collection_click, collection_list, color_by_trait, process_traits, trait_click;
+ var back_to_collections, collection_click, collection_list, color_by_trait, process_traits, root, this_trait_data, trait_click;
+
+ root = typeof exports !== "undefined" && exports !== null ? exports : this;
console.log("before get_traits_from_collection");
collection_list = null;
+ this_trait_data = null;
+
collection_click = function() {
var this_collection_url;
console.log("Clicking on:", $(this));
@@ -34,8 +38,10 @@
});
};
+ $.colorbox.close();
+
color_by_trait = function(trait_sample_data, textStatus, jqXHR) {
- return console.log('in color_by_trait:', trait_sample_data);
+ return root.bar_chart.color_by_trait(trait_sample_data);
};
process_traits = function(trait_data, textStatus, jqXHR) {
diff --git a/wqflask/wqflask/static/new/javascript/interval_mapping.coffee b/wqflask/wqflask/static/new/javascript/interval_mapping.coffee
index 78265f27..81db186b 100644
--- a/wqflask/wqflask/static/new/javascript/interval_mapping.coffee
+++ b/wqflask/wqflask/static/new/javascript/interval_mapping.coffee
@@ -66,30 +66,30 @@ $ ->
chr_lengths.push(this_length)
cumulative_chr_lengths.push(total_length + this_length)
total_length += this_length
-
+
console.log("chr_lengths: ", chr_lengths)
-
+
return [chr_lengths, cumulative_chr_lengths]
-
+
create_coordinates: () ->
chr_lengths = []
chr_seen = []
for result in js_data.qtl_results
- if result.locus.chr == "X"
+ if result.chr == "X"
chr_length = parseFloat(@chromosomes[20])
else
- chr_length = parseFloat(@chromosomes[result.locus.chr])
- if not(result.locus.chr in chr_seen)
- chr_seen.push(result.locus.chr)
+ chr_length = parseFloat(@chromosomes[result.chr])
+ if not(result.chr in chr_seen)
+ chr_seen.push(result.chr)
chr_lengths.push(chr_length)
- if result.locus.chr != "1"
+ if result.chr != "1"
@total_length += parseFloat(chr_lengths[chr_lengths.length - 2])
- @x_coords.push(@total_length + parseFloat(result.locus.Mb))
- @y_coords.push(result.lrs)
- @marker_names.push(result.locus.name)
+ @x_coords.push(@total_length + parseFloat(result.Mb))
+ @y_coords.push(result.lrs_value)
+ @marker_names.push(result.name)
@total_length += parseFloat(chr_lengths[chr_lengths.length-1])
#console.log("chr_lengths: ", chr_lengths)
-
+
create_svg: () ->
svg = d3.select("#interval_map")
.append("svg")
@@ -98,7 +98,7 @@ $ ->
.attr("height", @plot_height+@y_buffer)
return svg
-
+
create_graph: () ->
@add_border()
@add_x_axis()
@@ -107,13 +107,13 @@ $ ->
@fill_chr_areas()
@add_chr_labels()
@connect_markers()
-
+
add_border: () ->
border_coords = [[@y_buffer, @plot_height, @x_buffer, @x_buffer],
[@y_buffer, @plot_height, @plot_width, @plot_width],
[@y_buffer, @y_buffer, @x_buffer, @plot_width],
[@plot_height, @plot_height, @x_buffer, @plot_width]]
-
+
@svg.selectAll("line")
.data(border_coords)
.enter()
@@ -131,16 +131,16 @@ $ ->
return d[3]
)
.style("stroke", "#000")
-
+
create_scales: () ->
@x_scale = d3.scale.linear()
.domain([0, d3.max(@x_coords)])
.range([@x_buffer, @plot_width])
-
+
@y_scale = d3.scale.linear()
.domain([0, @y_max])
.range([@plot_height, @y_buffer])
-
+
create_x_axis_tick_values: () ->
tick_vals = []
for val in [25..@cumulative_chr_lengths[0]] when val%25 == 0
@@ -159,13 +159,13 @@ $ ->
#console.log("tick_vals:", tick_vals)
return tick_vals
-
+
add_x_axis: () ->
xAxis = d3.svg.axis()
.scale(@x_scale)
.orient("bottom")
.tickValues(@create_x_axis_tick_values())
-
+
next_chr = 1
tmp_tick_val = 0
xAxis.tickFormat((d) =>
@@ -183,7 +183,7 @@ $ ->
tick_val = tmp_tick_val
return (tick_val)
)
-
+
@svg.append("g")
.attr("class", "x_axis")
.attr("transform", "translate(0," + @plot_height + ")")
@@ -196,7 +196,7 @@ $ ->
)
#.attr("dy", "-1.0em")
-
+
add_y_axis: () ->
yAxis = d3.svg.axis()
.scale(@y_scale)
@@ -207,7 +207,7 @@ $ ->
.attr("class", "y_axis")
.attr("transform", "translate(" + @x_buffer + ",0)")
.call(yAxis)
-
+
add_chr_lines: () ->
@svg.selectAll("line")
.data(@cumulative_chr_lengths, (d) =>
@@ -215,10 +215,10 @@ $ ->
)
.enter()
.append("line")
- .attr("x1", @x_scale)
- .attr("x2", @x_scale)
.attr("y1", @y_buffer)
.attr("y2", @plot_height)
+ .attr("x1", @x_scale)
+ .attr("x2", @x_scale)
.style("stroke", "#ccc")
fill_chr_areas: () ->
@@ -239,8 +239,9 @@ $ ->
.attr("width", (d) =>
return @x_scale(d[0])
)
- .attr("height", @plot_height-@y_buffer)
-
+ .attr("height", @plot_height-@y_buffer)
+ .attr("fill", "white")
+
add_chr_labels: () ->
chr_names = []
for key of @chromosomes
@@ -263,12 +264,13 @@ $ ->
.attr("text-anchor", "middle")
.attr("font-family", "sans-serif")
.attr("font-size", "18px")
- .attr("fill", "grey")
-
+ #.attr("fill", "grey")
+
connect_markers: () ->
- @svg.selectAll("path")
+ @svg.selectAll("line")
.data(@plot_coordinates)
.enter()
+ .append("line")
.attr("x1", (d, i) =>
if i == 0
return @x_buffer
@@ -287,7 +289,9 @@ $ ->
.attr("y2", (d) =>
return @plot_height - ((@plot_height-@y_buffer) * d[1]/@y_max)
)
-
- console.time('Create manhattan plot')
+ .style("stroke", "black")
+
+ console.time('Create interval map')
+ console.log("TESTING")
new Interval_Map(600, 1200)
- console.timeEnd('Create manhattan plot') \ No newline at end of file
+ console.timeEnd('Create interval map') \ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/interval_mapping.js b/wqflask/wqflask/static/new/javascript/interval_mapping.js
index 5ae8ffab..3a2ce6d7 100644
--- a/wqflask/wqflask/static/new/javascript/interval_mapping.js
+++ b/wqflask/wqflask/static/new/javascript/interval_mapping.js
@@ -85,21 +85,21 @@
_ref = js_data.qtl_results;
for (_i = 0, _len = _ref.length; _i < _len; _i++) {
result = _ref[_i];
- if (result.locus.chr === "X") {
+ if (result.chr === "X") {
chr_length = parseFloat(this.chromosomes[20]);
} else {
- chr_length = parseFloat(this.chromosomes[result.locus.chr]);
+ chr_length = parseFloat(this.chromosomes[result.chr]);
}
- if (!(_ref1 = result.locus.chr, __indexOf.call(chr_seen, _ref1) >= 0)) {
- chr_seen.push(result.locus.chr);
+ if (!(_ref1 = result.chr, __indexOf.call(chr_seen, _ref1) >= 0)) {
+ chr_seen.push(result.chr);
chr_lengths.push(chr_length);
- if (result.locus.chr !== "1") {
+ if (result.chr !== "1") {
this.total_length += parseFloat(chr_lengths[chr_lengths.length - 2]);
}
}
- this.x_coords.push(this.total_length + parseFloat(result.locus.Mb));
- this.y_coords.push(result.lrs);
- this.marker_names.push(result.locus.name);
+ this.x_coords.push(this.total_length + parseFloat(result.Mb));
+ this.y_coords.push(result.lrs_value);
+ this.marker_names.push(result.name);
}
return this.total_length += parseFloat(chr_lengths[chr_lengths.length - 1]);
};
@@ -205,7 +205,7 @@
var _this = this;
return this.svg.selectAll("line").data(this.cumulative_chr_lengths, function(d) {
return d;
- }).enter().append("line").attr("x1", this.x_scale).attr("x2", this.x_scale).attr("y1", this.y_buffer).attr("y2", this.plot_height).style("stroke", "#ccc");
+ }).enter().append("line").attr("y1", this.y_buffer).attr("y2", this.plot_height).attr("x1", this.x_scale).attr("x2", this.x_scale).style("stroke", "#ccc");
};
Interval_Map.prototype.fill_chr_areas = function() {
@@ -220,7 +220,7 @@
}
}).attr("y", this.y_buffer).attr("width", function(d) {
return _this.x_scale(d[0]);
- }).attr("height", this.plot_height - this.y_buffer);
+ }).attr("height", this.plot_height - this.y_buffer).attr("fill", "white");
};
Interval_Map.prototype.add_chr_labels = function() {
@@ -237,12 +237,12 @@
return d[0];
}).attr("x", function(d) {
return _this.x_scale(d[2] - d[1] / 2);
- }).attr("y", this.plot_height * 0.1).attr("dx", "0em").attr("text-anchor", "middle").attr("font-family", "sans-serif").attr("font-size", "18px").attr("fill", "grey");
+ }).attr("y", this.plot_height * 0.1).attr("dx", "0em").attr("text-anchor", "middle").attr("font-family", "sans-serif").attr("font-size", "18px");
};
Interval_Map.prototype.connect_markers = function() {
var _this = this;
- return this.svg.selectAll("path").data(this.plot_coordinates).enter().attr("x1", function(d, i) {
+ return this.svg.selectAll("line").data(this.plot_coordinates).enter().append("line").attr("x1", function(d, i) {
if (i === 0) {
return _this.x_buffer;
} else {
@@ -258,15 +258,16 @@
return parseFloat(_this.x_buffer) + ((parseFloat(_this.plot_width) - parseFloat(_this.x_buffer)) * d[0] / parseFloat(_this.x_max));
}).attr("y2", function(d) {
return _this.plot_height - ((_this.plot_height - _this.y_buffer) * d[1] / _this.y_max);
- });
+ }).style("stroke", "black");
};
return Interval_Map;
})();
- console.time('Create manhattan plot');
+ console.time('Create interval map');
+ console.log("TESTING");
new Interval_Map(600, 1200);
- return console.timeEnd('Create manhattan plot');
+ return console.timeEnd('Create interval map');
});
}).call(this);
diff --git a/wqflask/wqflask/static/new/javascript/marker_regression.coffee b/wqflask/wqflask/static/new/javascript/marker_regression.coffee
index 2892987e..f5f13c27 100644
--- a/wqflask/wqflask/static/new/javascript/marker_regression.coffee
+++ b/wqflask/wqflask/static/new/javascript/marker_regression.coffee
@@ -49,10 +49,10 @@ $ ->
get_chr_lengths: () ->
###
- Gets a list of both individual and cumulative (the position of one on the graph
- is its own length plus the lengths of all preceding chromosomes) lengths in order
- to draw the vertical lines separating chromosomes and the chromosome labels
-
+ #Gets a list of both individual and cumulative (the position of one on the graph
+ #is its own length plus the lengths of all preceding chromosomes) lengths in order
+ #to draw the vertical lines separating chromosomes and the chromosome labels
+ #
###
console.log("@chromosomes: ", @chromosomes)
diff --git a/wqflask/wqflask/static/new/javascript/marker_regression.js b/wqflask/wqflask/static/new/javascript/marker_regression.js
index ffcf1a75..cdf37671 100644
--- a/wqflask/wqflask/static/new/javascript/marker_regression.js
+++ b/wqflask/wqflask/static/new/javascript/marker_regression.js
@@ -57,9 +57,10 @@
Manhattan_Plot.prototype.get_chr_lengths = function() {
/*
- Gets a list of both individual and cumulative (the position of one on the graph
- is its own length plus the lengths of all preceding chromosomes) lengths in order
- to draw the vertical lines separating chromosomes and the chromosome labels
+ #Gets a list of both individual and cumulative (the position of one on the graph
+ #is its own length plus the lengths of all preceding chromosomes) lengths in order
+ #to draw the vertical lines separating chromosomes and the chromosome labels
+ #
*/
var chr_lengths, cumulative_chr_lengths, key, this_length, total_length;
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.coffee b/wqflask/wqflask/static/new/javascript/show_trait.coffee
index 7d23345f..1df033d6 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.coffee
+++ b/wqflask/wqflask/static/new/javascript/show_trait.coffee
@@ -1,3 +1,5 @@
+root = exports ? this
+
console.log("start_b")
# this is our isNumber, do not confuse with the underscore.js one
@@ -62,10 +64,10 @@ $ ->
sample_lists = js_data.sample_lists
sample_group_types = js_data.sample_group_types
- new Bar_Chart(sample_lists[0])
+ $("#update_bar_chart.btn-group").button()
+ root.bar_chart = new Bar_Chart(sample_lists[0])
new Box_Plot(sample_lists[0])
-
$('.bar_chart_samples_group').change ->
$('#bar_chart').remove()
$('#bar_chart_container').append('<div id="bar_chart"></div>')
@@ -77,7 +79,8 @@ $ ->
else if group == "samples_all"
all_samples = sample_lists[0].concat sample_lists[1]
new Bar_Chart(all_samples)
-
+ #$(".btn-group").button()
+
$('.box_plot_samples_group').change ->
$('#box_plot').remove()
$('#box_plot_container').append('<div id="box_plot"></div>')
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 718e365a..90fa8228 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -1,9 +1,11 @@
// Generated by CoffeeScript 1.6.1
(function() {
- var Stat_Table_Rows, is_number,
+ var Stat_Table_Rows, is_number, root,
__hasProp = {}.hasOwnProperty,
__slice = [].slice;
+ root = typeof exports !== "undefined" && exports !== null ? exports : this;
+
console.log("start_b");
is_number = function(o) {
@@ -59,7 +61,8 @@
var block_by_attribute_value, block_by_index, block_outliers, change_stats_value, create_value_dropdown, edit_data_change, export_sample_table_data, get_sample_table_data, hide_no_value, hide_tabs, make_table, on_corr_method_change, populate_sample_attributes_values_dropdown, process_id, reset_samples_table, sample_group_types, sample_lists, show_hide_outliers, stats_mdp_change, update_stat_values;
sample_lists = js_data.sample_lists;
sample_group_types = js_data.sample_group_types;
- new Bar_Chart(sample_lists[0]);
+ $("#update_bar_chart.btn-group").button();
+ root.bar_chart = new Bar_Chart(sample_lists[0]);
new Box_Plot(sample_lists[0]);
$('.bar_chart_samples_group').change(function() {
var all_samples, group;
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
index 8571753e..df9bfc9d 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
@@ -53,6 +53,7 @@ $ ->
return false
$("#interval_mapping_compute").click(() =>
+ console.log("In interval mapping")
$("#progress_bar_container").modal()
url = "/interval_mapping"
form_data = $('#trait_data_form').serialize()
@@ -118,8 +119,12 @@ $ ->
composite_mapping_fields = ->
$(".composite_fields").toggle()
+ mapping_method_fields = ->
+ $(".mapping_method_fields").toggle()
+
$("#use_composite_choice").change(composite_mapping_fields)
+ $("#mapping_method_choice").change(mapping_method_fields)
#### Todo: Redo below so its like submit_special and requires no js hardcoding
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
index 1153b8ef..b474bd80 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -5,7 +5,7 @@
root = typeof exports !== "undefined" && exports !== null ? exports : this;
$(function() {
- var composite_mapping_fields, get_progress, submit_special, toggle_enable_disable, update_time_remaining,
+ var composite_mapping_fields, get_progress, mapping_method_fields, submit_special, toggle_enable_disable, update_time_remaining,
_this = this;
submit_special = function() {
var url;
@@ -64,6 +64,7 @@
};
$("#interval_mapping_compute").click(function() {
var form_data, url;
+ console.log("In interval mapping");
$("#progress_bar_container").modal();
url = "/interval_mapping";
form_data = $('#trait_data_form').serialize();
@@ -128,7 +129,11 @@
composite_mapping_fields = function() {
return $(".composite_fields").toggle();
};
+ mapping_method_fields = function() {
+ return $(".mapping_method_fields").toggle();
+ };
$("#use_composite_choice").change(composite_mapping_fields);
+ $("#mapping_method_choice").change(mapping_method_fields);
toggle_enable_disable = function(elem) {
return $(elem).prop("disabled", !$(elem).prop("disabled"));
};
diff --git a/wqflask/wqflask/templates/collections/list.html b/wqflask/wqflask/templates/collections/list.html
index ac621a61..354723d0 100644
--- a/wqflask/wqflask/templates/collections/list.html
+++ b/wqflask/wqflask/templates/collections/list.html
@@ -35,7 +35,7 @@
</table>
{# if "color_by_trait" in params #}
- <script type="text/javascript" src="/static/new/javascript/get_traits_from_collection.js"></script>
+<!-- <script type="text/javascript" src="/static/new/javascript/get_traits_from_collection.js"></script>-->
{# endif #}
</div>
diff --git a/wqflask/wqflask/templates/interval_mapping.html b/wqflask/wqflask/templates/interval_mapping.html
index 25de2dc1..e4e08388 100644
--- a/wqflask/wqflask/templates/interval_mapping.html
+++ b/wqflask/wqflask/templates/interval_mapping.html
@@ -1,7 +1,6 @@
{% extends "base.html" %}
{% block title %}Interval Mapping{% endblock %}
{% block css %}
- <link rel="stylesheet" type="text/css" href="/static/packages/jqplot/jquery.jqplot.min.css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/interval_mapping.css" />
<link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
<link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />
@@ -31,7 +30,9 @@
<tr>
<td>Index</td>
<td>LRS Score</td>
+ {% if method == "qtl_reaper" %}
<td>Additive Effect</td>
+ {% endif %}
<td>Chr</td>
<td>Mb</td>
<td>Locus</td>
@@ -41,11 +42,13 @@
{% for marker in qtl_results %}
<tr>
<td>{{ loop.index }}</td>
- <td>{{ marker.lrs|float }}</td>
+ <td>{{ marker.lrs_value|float }}</td>
+ {% if method == "qtl_reaper" %}
<td>{{ marker.additive|float }}</td>
- <td>{{ marker.locus.chr|int }}</td>
- <td>{{ marker.locus.Mb|float }}</td>
- <td>{{ marker.locus.name }}</td>
+ {% endif %}
+ <td>{{ marker.chr|int }}</td>
+ <td>{{ marker.Mb|float }}</td>
+ <td>{{ marker.name }}</td>
</tr>
{% endfor %}
</tbody>
@@ -63,7 +66,7 @@
</script>
<!--[if lt IE 9]>
- <script language="javascript" type="text/javascript" src="/static/packages/jqplot/excanvas.js"></script>
+<!-- <script language="javascript" type="text/javascript" src="/static/packages/jqplot/excanvas.js"></script>-->
<![endif]-->
<script language="javascript" type="text/javascript" src="http://d3js.org/d3.v3.min.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/javascript/interval_mapping.js"></script>
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index ec729e1c..86891bb0 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -2,6 +2,7 @@
{% block title %}Trait Data and Analysis{% endblock %}
{% block css %}
<link rel="stylesheet" type="text/css" href="/static/new/css/marker_regression.css" />
+ <link rel="stylesheet" type="text/css" href="/static/new/css/interval_mapping.css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/bar_chart.css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/box_plot.css" />
<link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
@@ -55,10 +56,11 @@
<script type="text/javascript" src="/static/new/javascript/stats.js"></script>
<script type="text/javascript" src="/static/new/javascript/box.js"></script>
+ <script type="text/javascript" src="/static/new/javascript/get_traits_from_collection.js"></script>
<script type="text/javascript" src="/static/new/javascript/bar_chart.js"></script>
<script type="text/javascript" src="/static/new/javascript/box_plot.js"></script>
- <script type="text/javascript" src="/static/new/javascript/get_traits_from_collection.js"></script>
- <script type="text/javascript" src="/static/new/javascript/show_trait.js"></script>
+
<script type="text/javascript" src="/static/new/javascript/show_trait_mapping_tools.js"></script>
+ <script type="text/javascript" src="/static/new/javascript/show_trait.js"></script>
<script type="text/javascript" src="/static/new/javascript/validation.js"></script>
{% endblock %}
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index a835a41b..58ee8982 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -17,6 +17,16 @@
<div class="tab-content">
<div class="tab-pane active" id="interval_mapping">
<div class="control-group">
+ <label for="mapping_method" class="control-label">Mapping Method</label>
+ <div class="controls" id="mapping_method_choice">
+ <select name="mapping_method">
+ <option value="qtl_reaper">H&K Regression</option>
+ <option value="pylmm">Linear Mixed</option>
+ </select>
+ </div>
+ </div>
+
+ <div class="control-group">
<label for="chromosome" class="control-label">Chromosome</label>
<div class="controls">
<select name="chromosome">
@@ -28,14 +38,14 @@
</div>
</div>
- <div class="control-group">
+ <div class="control-group mapping_method_fields">
<label for="mapping_permutations" class="control-label">Permutations (n)</label>
<div class="controls">
<input name="num_permutations" value="2000" type="text" />
</div>
</div>
- <div class="control-group">
+ <div class="control-group mapping_method_fields">
<label for="mapping_bootstraps" class="control-label"
title="Bootstrapping Resamples">Bootstrap (n)</label>
<div class="controls">
@@ -44,7 +54,7 @@
</div>
- <div class="control-group">
+ <div class="control-group mapping_method_fields">
<label class="control-label"><b>Composite Mapping</b></label>
<div class="controls" id="use_composite_choice">
<label class="radio inline">
diff --git a/wqflask/wqflask/templates/show_trait_statistics_new.html b/wqflask/wqflask/templates/show_trait_statistics_new.html
index 33538626..6d6b1d24 100644
--- a/wqflask/wqflask/templates/show_trait_statistics_new.html
+++ b/wqflask/wqflask/templates/show_trait_statistics_new.html
@@ -30,13 +30,23 @@
{% endfor %}
</select>
</div>
- {% endif %}
- <button type="button" class="btn" id="update_bar_chart">
+ {% endif %}
+ <div id="update_bar_chart" class="btn-group">
+ <button type="button" class="btn btn-default sort_by_name" value="name">
+ <i class="icon-resize-horizontal"></i> Sort By Name
+ </button>
+ <button type="button" class="btn btn-default sort_by_value" value="value">
+ <i class="icon-signal"></i> Sort By Value
+ </button>
+ </div>
+<!-- <button type="button" class="btn" id="update_bar_chart">
<i class="icon-resize-vertical"></i> Sort By Value
- </button>
- <button type="button" class="btn" id="color_by_trait">
- <i class="icon-tint"></i> Color by Trait
- </button>
+ </button>-->
+ <div class="btn-group">
+ <button type="button" class="btn" id="color_by_trait">
+ <i class="icon-tint"></i> Color by Trait
+ </button>
+ </div>
<div id="bar_chart_container">
<div id="bar_chart"></div>
</div>
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index b528f2b1..828199c5 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -258,6 +258,7 @@ def interval_mapping_page():
wanted = (
'trait_id',
'dataset',
+ 'mapping_method',
'chromosome',
'num_permutations',
'do_bootstraps',